Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019582.1 Corchorus olitorius cultivar O-4 contig19615, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 10992
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32


Found at i:120 original size:28 final size:28

Alignment explanation


    Indices: 64--120  Score: 69
    Period size: 28  Copynumber: 2.0  Consensus size: 28

         54 TTGGAAAGTG

                     **             *   
         64 AAATTACTATTTTACCCTTGGAGGGGTA
          1 AAATTACTAAATTACCCTTGGAGGAGTA

                               *  *     
         92 AAATTACTAAATTACCCTTTGATGAGTA
          1 AAATTACTAAATTACCCTTGGAGGAGTA

             
        120 A
          1 A

        121 TTTTATGAAT


Statistics
Matches: 24,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  28   24  1.00

ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Consensus pattern (28 bp):   
AAATTACTAAATTACCCTTGGAGGAGTA

Found at i:833 original size:27 final size:28

Alignment explanation


    Indices: 771--834  Score: 78
    Period size: 27  Copynumber: 2.3  Consensus size: 28

        761 AAATCACGTA

                          *             
        771 TTTGCCCTTGGTCGGCTAAAATTACCAT
          1 TTTGCCCTTGGTCGACTAAAATTACCAT

               *        *                
        799 TTTACCCTTGGTTGACT-AAATTA-CAGT
          1 TTTGCCCTTGGTCGACTAAAATTACCA-T

                     
        826 TTTGCCCTT
          1 TTTGCCCTT

        835 AAGCGTCGGA


Statistics
Matches: 31,  Mismatches: 4, Indels: 3
        0.82            0.11        0.08

Matches are distributed among these distances:
  26    2  0.06
  27   15  0.48
  28   14  0.45

ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41


Consensus pattern (28 bp):   
TTTGCCCTTGGTCGACTAAAATTACCAT

Found at i:6491 original size:22 final size:20

Alignment explanation


    Indices: 6466--6507  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       6456 GGCTATAATG

                                  
       6466 GGTTCAATCTTAGAGAGAGAAA
          1 GGTTCAA-C-TAGAGAGAGAAA

                *               
       6488 GGTTGAACTAGAGAGAGAAA
          1 GGTTCAACTAGAGAGAGAAA

       6508 TAAATGAGAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20   12  0.63
  21    1  0.05
  22    6  0.32

ACGTcount: A:0.43, C:0.07, G:0.31, T:0.19


Consensus pattern (20 bp):   
GGTTCAACTAGAGAGAGAAA
Done.